I’m not sure that I fully understand what you are asking, but a few comments:
If you want to crop or resample the image to get around the “same resolution” limitation, you should be able to do this, but you will will to calibrate the intrinsics with the same crop (or resampling) as you apply to the stereo calibration step. You can’t just use the intrinsics that you generated from the full size image and apply it to a cropped or resampled image.
If you must crop or resample, prefer the crop if possible.